SNaQ 1.1 simulations and empirical data scripts

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SNaQ 1.1 Simulations and Empirical Analysis Simulation study and empirical analysis evaluating computational improvements made in [SNaQ.jl](https://github.com/JuliaPhylo/SNaQ.jl) version 1.1, a Julia package for phylogenetic network inference using composite likelihood. This version introduces significant scalability improvements including parallelized quartet calculations, weighted quartet selection, and probabilistic network search, achieving up to 400% runtime improvements with maintained accuracy. Replication Instructions Given the breadth of parameters tested in these simulations and the computational intensity of each simulation individually, it is necessary to perform this study on a high throughput computing cluster. For this purpose, we utilize HT Condor. You will find that many of the scripts in this repository are specifically structured to work in a Condor environment and will not work properly outside of such an environment. See `condor/README.md` for replication instructions on a Condor cluster. Prior to this, original data must be obtained by the accompanying Dryad data repository. These simulations will take input data from the data/input/ folder and write output to the data/output/ folder to easy to read CSV files. Additionally, replicating the empirical results simply requires submitting the empirical-cui/condor/submit.submit file with the condor_submit command to an HT Condor submit node. Then, SNaQ.jl output files will be written to empirical-cui/condor/snaq_outputs/. Study Overview This repository contains the complete computational pipeline for: Simulation Study: Network inference performance and runtime analysis with networks consisting of either 10 or 20 taxa and either 1 or 3 hybrid nodes. Empirical Analysis: Application to Xiphophorus phylogenomic data from Cui et al. 2013 (https://doi.org/10.1111/evo.12099) Performance Evaluation: Runtime and accuracy comparisons between SNaQ.jl versions 1.0 and 1.1 Repository Structure Some of the following are contained in `zenodo.tar.gz` while others are missing because they are instead stored in the accompanying Dryad data repository. condor/ - HTCondor job submission and execution scripts data/ - Original networks, simulation outputs, and figures empirical-cui/ - Empirical analysis using Cui et al. 2013 Xiphophorus dataset pipelines/ - Core Julia simulation and analysis scripts results/ - Consolidated results from all simulation analyses scripts/ - Utility scripts for data processing software/ - External tools (IQ-TREE, Seq-Gen)

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